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Related Concept Videos

Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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Using PFP and ESG Protein Function Prediction Web Servers.

Qing Wei1, Joshua McGraw2, Ishita Khan1

  • 1Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.

Methods in Molecular Biology (Clifton, N.J.)
|April 29, 2017
PubMed
Summary
This summary is machine-generated.

Protein Function Prediction (PFP) and Extended Similarity Group (ESG) are novel webservers that improve protein function annotation by utilizing distantly related sequences. These tools enhance accuracy and coverage for unknown gene functions.

Keywords:
Automated function predictionBLASTGene OntologyGenome annotationProtein function predictionSequence analysis

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Computational Biology

Background:

  • Elucidating protein biological function is crucial in molecular biology and bioinformatics.
  • Traditional homology-based methods like BLAST and FASTA fail to annotate functions for proteins lacking obvious sequence similarity.
  • This limitation leaves many newly sequenced genes without functional interpretation.

Purpose of the Study:

  • To introduce novel webservers, Protein Function Prediction (PFP) and Extended Similarity Group (ESG), for improved protein function annotation.
  • To enhance the coverage and accuracy of functional annotation by leveraging distantly related sequences.
  • To provide user-friendly tools for interactive analysis of Gene Ontology (GO) annotations.

Main Methods:

  • Development and implementation of two webservers: Protein Function Prediction (PFP) and Extended Similarity Group (ESG).
  • Utilizing distantly related sequences to infer protein function.
  • Incorporating user-friendly visualizations for predicted GO terms and introducing NaviGO for interactive GO annotation analysis.

Main Results:

  • PFP and ESG demonstrated superior performance in benchmark studies and community assessments like CAFA1 and CAFA2.
  • The methods effectively improve function annotation coverage and accuracy, especially for proteins with distant homologs.
  • Webservers provide intuitive visualizations of predicted GO terms and interactive analysis capabilities.

Conclusions:

  • PFP and ESG are effective computational tools for advancing protein function prediction.
  • These webservers address limitations of traditional methods, offering broader functional annotation capabilities.
  • NaviGO complements PFP and ESG by facilitating interactive exploration of protein GO annotations.